X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 287 | Purified RNA was incubated at room temperature for 30 minutes in 25 mM Tris-HCl, pH 8.0, 50 mM potassium chloride, 10 mM magnesium chloride, 0.5 mM adenosylcobalamin prior to crystallization in 50 mM sodium cacodylate, 15% (v/v) PEG 400, 0.2 mM cobalt hexamine, 80 mM magnesium acetate, 1 mM spermine between pH 6.0 to pH 6.5 at 14C by vapor diffusion in a hanging drop format | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 5.51 | 77.69 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 118.282 | α = 90 |
| b = 118.282 | β = 90 |
| c = 261.547 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | RAYONIX MX-225 | Mirrors | 2013-06-03 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
| 1 | 3.253 | 39.213 | 92.8 | 0.16 | 0.162 | 0.025 | 0.996 | 18.2 | 47 | 15338 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 3.28 | 3.46 | 43.8 | 4.129 | 4.168 | 0.561 | 0.598 | 54 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MIRAS | FREE R-VALUE | 3.25 | 39.21 | 15338 | 785 | 86.3 | 0.263 | 0.26 | 0.279 | 0.27 | 129.1 | |||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| 0.693 | 0.347 | 0.693 | -2.248 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_1_deg | 8.013 |
| r_scangle_other | 3.118 |
| r_scangle_it | 3.117 |
| r_angle_other_deg | 2.165 |
| r_scbond_it | 1.847 |
| r_scbond_other | 1.847 |
| r_dihedral_angle_3_deg | 1.736 |
| r_angle_refined_deg | 0.807 |
| r_nbtor_refined | 0.253 |
| r_nbd_other | 0.22 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 3174 |
| Solvent Atoms | 48 |
| Heterogen Atoms | 179 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| SHARP | phasing |
| Coot | model building |
